DAMASK_EICMD/processing/legacy/DADF5toDREAM3D.py

139 lines
6.4 KiB
Python
Raw Normal View History

#!/usr/bin/env python3
import argparse
import os
import h5py
import numpy as np
import damask
class AttributeManagerNullterm(h5py.AttributeManager):
"""
Attribute management for DREAM.3D hdf5 files.
String attribute values are stored as fixed-length string with NULLTERM
References
----------
https://stackoverflow.com/questions/38267076
https://stackoverflow.com/questions/52750232
"""
def create(self, name, data, shape=None, dtype=None):
if isinstance(data,str):
tid = h5py.h5t.C_S1.copy()
tid.set_size(len(data + ' '))
super().create(name=name,data=data+' ',dtype = h5py.Datatype(tid))
else:
super().create(name=name,data=data,shape=shape,dtype=dtype)
h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
# --------------------------------------------------------------------
# Crystal structure specifications
# --------------------------------------------------------------------
Crystal_structures = {'fcc': 1,
'bcc': 1,
'hcp': 0,
'bct': 7,
'ort': 6} #TODO: is bct Tetragonal low/Tetragonal high?
Phase_types = {'Primary': 0} #further additions to these can be done by looking at 'Create Ensemble Info' filter
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = argparse.ArgumentParser(description='Creating a file for DREAM3D from DAMASK data')
2020-03-18 18:14:39 +05:30
parser.add_argument('filenames', nargs='+',
help='DADF5 files')
parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
2020-03-18 18:14:39 +05:30
help='name of subdirectory relative to the location of the DADF5 file to hold output')
parser.add_argument('--inc',nargs='+',
help='Increment for which DREAM3D to be used, eg. 25',type=int)
options = parser.parse_args()
for filename in options.filenames:
2020-03-17 06:19:47 +05:30
f = damask.Result(filename)
N_digits = int(np.floor(np.log10(int(f.increments[-1][3:]))))+1
2020-03-17 06:19:47 +05:30
f.pick('increments',options.inc)
for inc in damask.util.show_progress(f.iterate('increments'),len(f.selection['increments'])):
2020-03-17 06:19:47 +05:30
dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
try:
os.mkdir(dirname)
except FileExistsError:
pass
o = h5py.File(dirname + '/' + os.path.splitext(filename)[0] \
2020-03-19 16:21:30 +05:30
+ '_inc_{}.dream3D'.format(inc[3:].zfill(N_digits)),'w')
2020-03-17 06:19:47 +05:30
o.attrs['DADF5toDREAM3D'] = '1.0'
o.attrs['FileVersion'] = '7.0'
2020-03-17 06:19:47 +05:30
for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
o.create_group(g)
data_container_label = 'DataContainers/ImageDataContainer'
2020-03-17 06:19:47 +05:30
cell_data_label = data_container_label + '/CellData'
# Phase information of DREAM.3D is constituent ID in DAMASK
o[cell_data_label + '/Phases'] = f.get_constituent_ID().reshape(tuple(f.grid)+(1,))
2020-03-17 06:19:47 +05:30
DAMASK_quaternion = f.read_dataset(f.get_dataset_location('orientation'))
# Convert: DAMASK uses P = -1, DREAM.3D uses P = +1. Also change position of imagninary part
DREAM_3D_quaternion = np.hstack((-DAMASK_quaternion['x'],-DAMASK_quaternion['y'],-DAMASK_quaternion['z'],
DAMASK_quaternion['w'])).astype(np.float32)
o[cell_data_label + '/Quats'] = DREAM_3D_quaternion.reshape(tuple(f.grid)+(4,))
2020-03-17 06:19:47 +05:30
# Attributes to CellData group
o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32)
o[cell_data_label].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
2020-03-17 06:19:47 +05:30
# Common Attributes for groups in CellData
for group in ['/Phases','/Quats']:
o[cell_data_label + group].attrs['DataArrayVersion'] = np.array([2],np.int32)
o[cell_data_label + group].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*f.grid)
2020-03-17 06:19:47 +05:30
o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray<int32_t>'
o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
2020-03-17 06:19:47 +05:30
o[cell_data_label + '/Quats'].attrs['ComponentDimensions'] = np.array([4],np.uint64)
o[cell_data_label + '/Quats'].attrs['ObjectType'] = 'DataArray<float>'
2020-03-17 06:19:47 +05:30
o[cell_data_label + '/Quats'].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
2020-03-17 06:19:47 +05:30
# Create EnsembleAttributeMatrix
ensemble_label = data_container_label + '/EnsembleAttributeMatrix'
2020-03-17 06:19:47 +05:30
# Data CrystalStructures
o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999,\
2020-03-17 16:52:48 +05:30
Crystal_structures[f.get_crystal_structure()]])).reshape(2,1)
o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999,Phase_types['Primary']])).reshape(2,1) # ToDo
2020-03-17 06:19:47 +05:30
# Attributes Ensemble Matrix
o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32)
o[ensemble_label].attrs['TupleDimensions'] = np.array([2], np.uint64)
2020-03-17 06:19:47 +05:30
# Attributes for data in Ensemble matrix
for group in ['CrystalStructures','PhaseTypes']: # 'PhaseName' not required MD: But would be nice to take the phase name mapping
o[ensemble_label+'/'+group].attrs['ComponentDimensions'] = np.array([1],np.uint64)
o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = 'x=2'
o[ensemble_label+'/'+group].attrs['DataArrayVersion'] = np.array([2],np.int32)
o[ensemble_label+'/'+group].attrs['ObjectType'] = 'DataArray<uint32_t>'
o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([2],np.uint64)
2020-03-17 06:19:47 +05:30
geom_label = data_container_label + '/_SIMPL_GEOMETRY'
2020-03-17 06:19:47 +05:30
o[geom_label + '/DIMENSIONS'] = np.int64(f.grid)
o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3))
o[geom_label + '/SPACING'] = np.float32(f.size)
2020-03-17 06:19:47 +05:30
o[geom_label].attrs['GeometryName'] = 'ImageGeometry'
o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry'
o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32)
o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32)